The fifth seeded Indian pair, making its debut as a pair at the elite event, lost the title clash 5-7 6-3 3-10 to the sixth seeded combine in one hour and 30 minutes late last night.
No Indian pair has ever won the year-end finale although Leander Paes and Bhupathi reached the finals thrice together.
Now it's the fifth time that Bhupathi has ended runners-up at the event, where world's top-8 teams compete for the championship. With Paes he ended runner-up in 1997, 1999 and 2000 and with Max Mirnyi in 2010.
Bhupathi and Bopanna had beaten Paes and his Czech partner Radek Stepanek in the semifinals.
Bhupathi and Bopanna, thus, end the 2012 season and their partnership with two titles -- Dubai and the Paris Masters.
Bhupathi will partner Daniel Nestor in the next season while Bopanna is yet to confirm his teammate.
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Granollers and Lopez became the second Spanish team to win the season-ending championships. The only other Spanish duo to win the championship are Juan Gisbert Sr and Manuel Orantes in 1975 at Stockholm.
The Spaniards took a 2-1 lead in the first set, after Granollers hit three successive forehands at Bopanna, who hit a backhand volley into the net on the deciding point.